Invoking:
  getsize /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa 1> $metrics
Finished invoke:
  name: count_seqs  status: 0  time: 0.069094
Invoking:
  fasta-most -min 50 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa 1> $metrics
Finished invoke:
  name: most_seqs  status: 0  time: 0.062912
Invoking:
  fasta-center -dna -len 100 < /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-centered
Finished invoke:
  name: center_seqs  status: 0  time: 0.0970220000000001
Invoking:
  fasta-shuffle-letters /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-centered /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
Finished invoke:
  name: shuffle_seqs  status: 0  time: 0.021474
Invoking:
  fasta-subsample /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-centered 600 -rest /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-discarded -seed 1 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-sampled
Finished invoke:
  name: sample_seqs  status: 0  time: 0.077895
Invoking:
  fasta-get-markov -nostatus -nosummary -dna -m 1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background
Finished invoke:
  name: bg  status: 0  time: 0.018731
Invoking:
  meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background -dna -revcomp -nostatus
Finished invoke:
  name: meme  status: 0  time: 993.144436
Invoking:
  dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-shuffled
Finished invoke:
  name: dreme  status: 0  time: 39.220258
Invoking:
  centrimo -seqlen 508 -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/centrimo_out -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml
Finished invoke:
  name: centrimo  status: 0  time: 0.146359
Invoking:
  tomtom -verbosity 1 -text -thresh 0.1 /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/combined.meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/combined.meme 1> /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/motif_alignment.txt
Finished invoke:
  name: align  status: 0  time: 0.224953
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/spamo_out_1 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background -primary SGGRHTCGAACCSVBGACCTY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml
Finished invoke:
  name: spamo1  status: 0  time: 0.557325
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/spamo_out_2 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background -primary DTGGYCBAGTKGKTWAAGSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml
Finished invoke:
  name: spamo2  status: 0  time: 0.507783
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/spamo_out_3 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background -primary ARWRAAARAADAARAAAAARM /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml
Finished invoke:
  name: spamo3  status: 0  time: 0.576102
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/spamo_out_4 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background -primary RGAAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml
Finished invoke:
  name: spamo4  status: 0  time: 0.58774
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/spamo_out_5 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background -primary ACCGW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml
Finished invoke:
  name: spamo5  status: 0  time: 0.6312
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/spamo_out_6 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background -primary ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml
Finished invoke:
  name: spamo6  status: 0  time: 0.332755
Invoking:
  spamo -verbosity 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/spamo_out_7 -bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background -primary CTKACCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml
Finished invoke:
  name: spamo7  status: 0  time: 0.319939
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/fimo_out_1 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background --motif SGGRHTCGAACCSVBGACCTY /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa
Finished invoke:
  name: fimo1  status: 0  time: 0.415313
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background --motif DTGGYCBAGTKGKTWAAGSS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa
Finished invoke:
  name: fimo2  status: 0  time: 0.404483
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/fimo_out_3 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background --motif ARWRAAARAADAARAAAAARM /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme_out/meme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa
Finished invoke:
  name: fimo3  status: 0  time: 0.429576
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background --motif RGAAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa
Finished invoke:
  name: fimo4  status: 0  time: 0.278086
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background --motif ACCGW /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa
Finished invoke:
  name: fimo5  status: 0  time: 0.287007
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/fimo_out_6 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background --motif ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa
Finished invoke:
  name: fimo6  status: 0  time: 0.318288
Invoking:
  fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/background --motif CTKACCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/BY4741--YAP3.fa
Finished invoke:
  name: fimo7  status: 0  time: 0.293851
Writing output
Invoking:
  meme-chip_html_to_tsv /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/meme-chip.html /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/summary.tsv
Finished invoke:
  name: summary  status: 0  time: 0.154912
Done